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Background  Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using  DORNRÖSCHEN-LIKE::GFP  to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in  apetala1 cauliflower  double mutants, which overproliferate IMs.    Results  Within the lateral organ founder-cell population at the inflorescence meristem, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. Additional differentially expressed transcripts are involved in polarity generation and boundary formation, and in epigenetic and post-translational changes. However, only subtle transcriptional reprogramming within the global auxin network was observed.    Conclusions  The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. However, contrary to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, auxin response might play a minor role in the earliest stages of lateral floral initiation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3189-x) contains supplementary material, which is available to authorized users.

The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem